Anopheles gambiae vs Anopheles dirus LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles dirus (Anopheles dirus, AdirW1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1506. Anopheles gambiae was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 207,728

Genome coverage (bp) Coding exon coverage (bp)
Anopheles gambiae

Uncovered: 160,228,457 out of 273,109,044
Covered: 112,880,587 out of 273,109,044

Uncovered: 597,743 out of 20,801,863
Matches: 16,032,445 out of 20,801,863
Mismatches: 3,700,373 out of 20,801,863
Insertions: 471,302 out of 20,801,863

Anopheles dirus

Uncovered: 114,477,252 out of 216,307,690
Covered: 101,830,438 out of 216,307,690

Uncovered: 594,109 out of 21,008,310
Matches: 16,172,682 out of 21,008,310
Mismatches: 3,828,262 out of 21,008,310
Insertions: 413,257 out of 21,008,310

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)--ambiguous=iupac

Chunking parameters

Anopheles gambiae Anopheles dirus
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}